※峰识别(peak calling)工具包括:MACS2和HOMER(适用于ChIP-seq和ATAC-seq)、HMMRATAC(针对于ATAC-seq)、exomePeak(针对m6A-seq)。 ※差异峰分析(peak differential analysis)工具包括:HOMER、DiffBind,它们是consensus peak-based工具,假设数据分布是负二项分布。consensus peak是指:不同生物学样本重复得到的peaks进行...
NAME_peaks.xls包含peak信息的tab分割的文件,前几行会显示callpeak时的命令。输出信息包含: 染色体号 peak起始位点 peak结束位点 peak区域长度 peak的峰值位点(summit position) peak 峰值的高度(pileup height at peak summit, -log10(pvalue) for the peak summit) peak的富集倍数(相对于random Poisson distributi...
包含peak信息的tab分割的文件,前几行会显示callpeak时的命令。输出信息包含: 染色体号 peak起始位点 peak结束位点 peak区域长度 peak的峰值位点(summit position) peak 峰值的高度(pileup height at peak summit, -log10(pvalue) for the peak summit) peak的富集倍数(相对于random Poisson distribution with local ...
MACS2使用 \lambda_{local} 计算peak 的 p 值,没有 control 则没有 \lambda_{1k}。 输入的数据为 2.3.3 samtools sort 后的文件。 #有control数据 for i in *.bam do macs2 callpeak -f BAM -c control.bam -t $i -n $i -g hs --outdir ../macs2/ --bdg -q 0.05 done #没有control...
callpeak-Options Variousoptionstoindicate/controlinput,output,peakmodellingandpeakcallingmacs2callpeakusage:macs2callpeak[-h]-tTFILE[TFILE...][-c[CFILE[CFILE...]]][-f{AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE,BAMPE}][-gGSIZE][--keep-dupKEEPDUPLICATES][--buffer-sizeBUFFER_SIZE]...
treat_pileup.bdg control_lambda.bd g refinepeaksrefinepeak.bed randsample filterdup predictd pileuppileup.bdg bdgpeakcall OUTPUT callpeak Options Various options to indicate/control input, output, peak modelling and peak calling macs2 callpeak usage: macs2 callpeak [h] t TFILE&...
44、sing MACS test different settings,Run 1: Using default settings Run 2: Call summits Run 3: Adjust model band width Run 4: Adjust mfold limits From command history, find the previous macs2 command and edit the red parts: macs2 callpeak -t seq/treat_chr3.sam -c seq/input_chr3.sam...
The peak call parameters can be explicitly specified for custom control. Broad, or gapped-peak, calls may also be made if desired. Intersect peaks Use intersect_peaks to intersect the peaks from each ChIP sample into a master list of peaks across all ChIP conditions, as well as generate a ...
In this case, I would suggest you to generate treatment bdg files for two condition from callpeak or pileup function, then compare them directly using bdgcmp. Hi Tao Liu, Could you please elaborate on how to compare the treatment bdg files for two conditions from callpeak or pileup ...
macs2 callpeak -t seq/treat_chr3.sam -c seq/input_chr3.sam --outdir macsout_user ID --call-summits --bw 200 –n bw200.cs Using MACS – test different settings Run 1: Using default settings Run 2: Call summits Run 3: Adjust model band width Run 4: Adjust mfold limits From ...